title: MPRA from HepG2 (ENCLB546YEI)

description:
https://www.encodeproject.org/experiments/ENCSR736XUK/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR736XUK
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB546YEI
fragmentation methods: none

value: male

value: hepatocellular carcinoma

value: 15 years

value: ENCBS127VZI at ENCODE; https://www.encodeproject.org/ENCBS127VZI/


title: MPRA from SK-N-SH (ENCLB066LYQ)

status: Public on May 07 2024

type: SRA

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR742AAP/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR742AAP
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB066LYQ
fragmentation methods: none

library_source: transcriptomic

data_processing: See GSM*_README.txt supplementary file linked below

molecule: total RNA

organism: Homo sapiens

source_name: Homo sapiens SK-N-SH cell line genetically modified (episome) using transient transfection, 24 hours post-nucleic acid delivery time

tag: line

value: SK-N-SH

value: cell line

tag: biosample encode accession

tag: collection date

value: not applicable

tag: geographic location

tag: encode accession

tag: Sex

value: female

tag: health state

value: Metastatic neuroblastoma from bone marrow

tag: dev stage

value: child

tag: age

value: 4 years

tag: passage number

tag: lab

value: Ryan Tewhey, JAX

tag: source

value: ATCC

tag: link

value: ENCBS762DSL at ENCODE; https://www.encodeproject.org/ENCBS762DSL/


title: Brain, Paxton limnetic, conspecific courtship, trial 57

city: University Park

first: Jason

last: Keagy

state: PA

address: 410 Forest Resources Bldg

department: Ecosystem Science and Management

institute: Penn State University

data_processing:
Bioinformatic analyses were carried out using the computational resources of the Texas Advanced Computing Center (TACC).
Reads from all eight lanes were combined for each uniquely barcoded individual, separately for forward and reverse reads.
We conducted quality control checks using fastqc (v0.11.1).
We then ran Trimmomatic (v0.33)to remove a small amount of adapter contamination.
Next, reads were aligned to the Gasterosteus aculeatus Ensembl BROAD S1 draft genome (version 78) using bwa (v0.7.7).
Samtools (v1.2) was used to convert sam to bam files, and then sort and index them.
These sorted and indexed bam files were then passed to bedtools (v2.23.0) to count gene transcripts.
Assembly: Gasterosteus aculeatus Ensembl BROAD S1 draft genome (version 78)
Supplementary files format and content: Tab deliminated text file containing raw ead counts with samples in columns and genes in rows.

molecule: polyA RNA

organism: Gasterosteus aculeatus

source_name: whole brain

extract_protocol:
After 20 min of time with the courting male/ female social control or spawning (whichever came first), the female subject was killed by rapid cervical dissection, and the brain was immediately dissected under a microscope in a Sylgaard 184-lined petri-dish filled with a Ringer’s solution. Brains were stored overnight in RNAlater at 4°C and then transferred to -20°C until RNA extraction. Brains were shipped on dry ice from Michigan State University to The University of Texas at Austin where RNA was extracted using the Maxwell 16 LEV simplyRNA Tissue Kit, which utilizes a robot to increase consistency.
At the UT Austin Genomic Sequencing and Analysis Facility (GSAF) each sample (all with RIN > 7.8, 8.8 ± 0.4 mean ± SD, 11 samples do not have RIN scores) was prepared for RNA-seq using PolyA mRNA capture and given a unique barcode. A single library of all multiplexed samples was sequenced across eight lanes of an Illumina Hiseq 2500 with 2x50 PE chemistry.

tag: tissue

value: whole brain

tag: population

value: Paxton limnetic

tag: treatment

value: conspecific courtship


title: Brain, Priest limnetic, conspecific courtship, trial 52

value: Priest limnetic


title: Brain, Paxton limnetic, conspecific courtship, trial 55


title: Brain, Priest limnetic, female social control, trial 53

value: female social control


title: MPRA from HepG2 (ENCLB362GLF)

description:
https://www.encodeproject.org/experiments/ENCSR736XUK/
***************
biological replicate number: 5
technical replicate number: 1
description:
experiment encode accession: ENCSR736XUK
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB362GLF
fragmentation methods: none

source_name: Homo sapiens HepG2 cell line genetically modified (episome) using transient transfection, 24 hours post-nucleic acid delivery time

value: male

value: hepatocellular carcinoma

value: 15 years

value: ENCBS741JAB at ENCODE; https://www.encodeproject.org/ENCBS741JAB/


title: MPRA from HepG2 (ENCLB490SCK)

description:
https://www.encodeproject.org/experiments/ENCSR736XUK/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR736XUK
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB490SCK
fragmentation methods: none

value: cell line

value: not applicable

value: ENCBS774YOM at ENCODE; https://www.encodeproject.org/ENCBS774YOM/


title: MPRA from HepG2 (ENCLB231SLV)

description:
https://www.encodeproject.org/experiments/ENCSR736XUK/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR736XUK
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB231SLV
fragmentation methods: none

value: child

value: ENCBS172TFD at ENCODE; https://www.encodeproject.org/ENCBS172TFD/


title: Brain, Paxton limnetic, female social control, trial 51

value: female


title: MPRA from SK-N-SH (ENCLB915PZH)

description:
https://www.encodeproject.org/experiments/ENCSR742AAP/
***************
biological replicate number: 5
technical replicate number: 1
description:
experiment encode accession: ENCSR742AAP
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB915PZH
fragmentation methods: none

value: SK-N-SH

value: Metastatic neuroblastoma from bone marrow

value: 4 years

value: Ryan Tewhey, JAX

value: ATCC

value: ENCBS708HKU at ENCODE; https://www.encodeproject.org/ENCBS708HKU/


title: Brain, Paxton limnetic, heterospecific courtship, trial 49

value: whole brain

value: Paxton limnetic

value: heterospecific courtship


title: MPRA from A549 (ENCLB597WTI)

description:
https://www.encodeproject.org/experiments/ENCSR729IRS/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR729IRS
assay title: MPRA
assembly: hg19, GRCh38
possible controls: ENCSR915INT
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB597WTI
fragmentation methods: none

source_name: Homo sapiens A549 cell line genetically modified (episome) using transient transfection, 24 hours post-nucleic acid delivery time

value: male

value: adult

value: 58 years

value: ENCBS265MVN at ENCODE; https://www.encodeproject.org/ENCBS265MVN/


title: Brain, Priest limnetic, female social control, trial 45

value: Priest limnetic

value: female social control


title: Brain, Priest limnetic, female social control, trial 66


title: MPRA from A549 (ENCLB737QPS)

description:
https://www.encodeproject.org/experiments/ENCSR729IRS/
***************
biological replicate number: 5
technical replicate number: 1
description:
experiment encode accession: ENCSR729IRS
assay title: MPRA
assembly: hg19, GRCh38
possible controls: ENCSR915INT
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB737QPS
fragmentation methods: none

value: cell line

value: not applicable

value: ENCBS579OLY at ENCODE; https://www.encodeproject.org/ENCBS579OLY/


title: Brain, Priest limnetic, heterospecific courtship, trial 44

value: female


title: MPRA from A549 (ENCLB552YWY)

description:
https://www.encodeproject.org/experiments/ENCSR729IRS/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR729IRS
assay title: MPRA
assembly: hg19, GRCh38
possible controls: ENCSR915INT
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB552YWY
fragmentation methods: none

value: ENCBS568TJC at ENCODE; https://www.encodeproject.org/ENCBS568TJC/


title: Brain, Paxton limnetic, heterospecific courtship, trial 41


title: MPRA from HepG2 (ENCLB416EUL)

description:
https://www.encodeproject.org/experiments/ENCSR712VZT/
***************
biological replicate number: 7
technical replicate number: 1
description:
experiment encode accession: ENCSR712VZT
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB416EUL
fragmentation methods: none

value: hepatocellular carcinoma

value: child

value: 15 years

value: Ryan Tewhey, JAX

value: ENCBS868NJA at ENCODE; https://www.encodeproject.org/ENCBS868NJA/


title: MPRA from HepG2 (ENCLB305PII)

description:
https://www.encodeproject.org/experiments/ENCSR736XUK/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR736XUK
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB305PII
fragmentation methods: none

value: ATCC

value: ENCBS961AVC at ENCODE; https://www.encodeproject.org/ENCBS961AVC/


title: Brain, Paxton limnetic, conspecific courtship, trial 40

value: whole brain

value: Paxton limnetic

value: conspecific courtship


title: Brain, Paxton limnetic, heterospecific courtship, trial 37

value: heterospecific courtship


title: Brain, Priest limnetic, conspecific courtship, trial 38

value: Priest limnetic


title: Brain, Paxton benthic, female social control, trial 39

value: Paxton benthic

value: female social control


title: MPRA from HepG2 (ENCLB811FNF)

description:
https://www.encodeproject.org/experiments/ENCSR712VZT/
***************
biological replicate number: 5
technical replicate number: 1
description:
experiment encode accession: ENCSR712VZT
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB811FNF
fragmentation methods: none

value: cell line

value: not applicable

value: male

value: ENCBS109SJZ at ENCODE; https://www.encodeproject.org/ENCBS109SJZ/


title: MPRA from HepG2 (ENCLB416KEH)

description:
https://www.encodeproject.org/experiments/ENCSR712VZT/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR712VZT
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB416KEH
fragmentation methods: none

value: hepatocellular carcinoma

value: child

value: ENCBS551QJW at ENCODE; https://www.encodeproject.org/ENCBS551QJW/


title: MPRA from HepG2 (ENCLB201LVM)

description:
https://www.encodeproject.org/experiments/ENCSR712VZT/
***************
biological replicate number: 6
technical replicate number: 1
description:
experiment encode accession: ENCSR712VZT
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB201LVM
fragmentation methods: none

value: 15 years

value: Ryan Tewhey, JAX

value: ENCBS403PMP at ENCODE; https://www.encodeproject.org/ENCBS403PMP/


title: MPRA from A549 (ENCLB970TPB)

description:
https://www.encodeproject.org/experiments/ENCSR729IRS/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR729IRS
assay title: MPRA
assembly: hg19, GRCh38
possible controls: ENCSR915INT
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB970TPB
fragmentation methods: none

value: adult

value: 58 years

value: ATCC

value: ENCBS172IDH at ENCODE; https://www.encodeproject.org/ENCBS172IDH/


title: MPRA from K562 (ENCLB603VOB)

description:
https://www.encodeproject.org/experiments/ENCSR697PNZ/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR697PNZ
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB603VOB
fragmentation methods: none

source_name: Homo sapiens K562 cell line genetically modified (episome) using transient transfection, 24 hours post-nucleic acid delivery time

value: female

value: chronic myelogenous leukemia (CML)

value: 53 years

value: ENCBS562JOC at ENCODE; https://www.encodeproject.org/ENCBS562JOC/


title: MPRA from HepG2 (ENCLB567XSB)

description:
https://www.encodeproject.org/experiments/ENCSR712VZT/
***************
biological replicate number: 8
technical replicate number: 1
description:
experiment encode accession: ENCSR712VZT
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB567XSB
fragmentation methods: none

value: cell line

value: not applicable

value: ENCBS457LTE at ENCODE; https://www.encodeproject.org/ENCBS457LTE/


title: Brain, Paxton benthic, heterospecific courtship, trial 31

value: whole brain

value: Paxton benthic

value: heterospecific courtship


title: Brain, Paxton benthic, conspecific courtship, trial 34

value: conspecific courtship


title: MPRA from HepG2 (ENCLB905XSW)

description:
https://www.encodeproject.org/experiments/ENCSR712VZT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR712VZT
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB905XSW
fragmentation methods: none

value: male

value: hepatocellular carcinoma

value: child

value: 15 years

value: Ryan Tewhey, JAX

value: ENCBS033EMK at ENCODE; https://www.encodeproject.org/ENCBS033EMK/


title: Brain, Paxton limnetic, heterospecific courtship, trial 30

value: Paxton limnetic

value: female


title: Brain, Priest limnetic, female social control, trial 29

value: Priest limnetic

value: female social control


title: Brain, Paxton benthic, conspecific courtship, trial 43


title: MPRA from A549 (ENCLB149XBM)

description:
https://www.encodeproject.org/experiments/ENCSR729IRS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR729IRS
assay title: MPRA
assembly: hg19, GRCh38
possible controls: ENCSR915INT
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB149XBM
fragmentation methods: none

value: cell line

value: adult

value: 58 years

value: ATCC

value: ENCBS132ELW at ENCODE; https://www.encodeproject.org/ENCBS132ELW/


title: Brain, Priest limnetic, female social control, trial 27

value: whole brain


title: MPRA from K562 (ENCLB986JHI)

description:
https://www.encodeproject.org/experiments/ENCSR697PNZ/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR697PNZ
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB986JHI
fragmentation methods: none

value: not applicable

value: chronic myelogenous leukemia (CML)

value: 53 years

value: ENCBS090ZLO at ENCODE; https://www.encodeproject.org/ENCBS090ZLO/


title: MPRA from K562 (ENCLB151NGW)

description:
https://www.encodeproject.org/experiments/ENCSR697PNZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR697PNZ
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB151NGW
fragmentation methods: none

value: ENCBS299QQG at ENCODE; https://www.encodeproject.org/ENCBS299QQG/


title: Brain, Paxton limnetic, heterospecific courtship, trial 26

value: heterospecific courtship


title: MPRA from K562 (ENCLB349WSX)

description:
https://www.encodeproject.org/experiments/ENCSR697PNZ/
***************
biological replicate number: 5
technical replicate number: 1
description:
experiment encode accession: ENCSR697PNZ
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB349WSX
fragmentation methods: none

value: Ryan Tewhey, JAX

value: ENCBS545REY at ENCODE; https://www.encodeproject.org/ENCBS545REY/


title: MPRA from HepG2 (ENCLB109VOA)

description:
https://www.encodeproject.org/experiments/ENCSR712VZT/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR712VZT
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB109VOA
fragmentation methods: none

value: male

value: hepatocellular carcinoma

value: child

value: 15 years

value: ENCBS685DGN at ENCODE; https://www.encodeproject.org/ENCBS685DGN/


title: Brain, Priest limnetic, heterospecific courtship, trial 23

value: Priest limnetic

value: female


title: Brain, Paxton limnetic, female social control, trial 33

value: Paxton limnetic

value: female social control


title: MPRA from HepG2 (ENCLB321EKG)

description:
https://www.encodeproject.org/experiments/ENCSR712VZT/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR712VZT
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB321EKG
fragmentation methods: none

value: cell line

value: not applicable

value: ATCC

value: ENCBS050RLC at ENCODE; https://www.encodeproject.org/ENCBS050RLC/


title: MPRA from HepG2 (ENCLB418CNH)

description:
https://www.encodeproject.org/experiments/ENCSR694VUM/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR694VUM
assay title: MPRA
possible controls: ENCSR556IED
encode release date: 2024-04-25
lab: Ryan Tewhey, JAX
library encode accession: ENCLB418CNH
fragmentation methods: none

value: ENCBS190SKH at ENCODE; https://www.encodeproject.org/ENCBS190SKH/


title: Brain, Paxton limnetic, female social control, trial 25

value: whole brain


title: MPRA from K562 (ENCLB762OIO)

description:
https://www.encodeproject.org/experiments/ENCSR697PNZ/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR697PNZ
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB762OIO
fragmentation methods: none

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 years

value: Ryan Tewhey, JAX

value: ENCBS824CVR at ENCODE; https://www.encodeproject.org/ENCBS824CVR/


title: MPRA from HepG2 (ENCLB937KET)

description:
https://www.encodeproject.org/experiments/ENCSR694VUM/
***************
biological replicate number: 5
technical replicate number: 1
description:
experiment encode accession: ENCSR694VUM
assay title: MPRA
possible controls: ENCSR556IED
encode release date: 2024-04-25
lab: Ryan Tewhey, JAX
library encode accession: ENCLB937KET
fragmentation methods: none

value: male

value: hepatocellular carcinoma

value: child

value: 15 years

value: ENCBS987KLT at ENCODE; https://www.encodeproject.org/ENCBS987KLT/


title: Brain, Paxton limnetic, conspecific courtship, trial 20

value: Paxton limnetic

value: female

value: conspecific courtship


title: Brain, Priest limnetic, heterospecific courtship, trial 18

value: Priest limnetic

value: heterospecific courtship


title: MPRA from HepG2 (ENCLB556DCZ)

description:
https://www.encodeproject.org/experiments/ENCSR694VUM/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR694VUM
assay title: MPRA
possible controls: ENCSR556IED
encode release date: 2024-04-25
lab: Ryan Tewhey, JAX
library encode accession: ENCLB556DCZ
fragmentation methods: none

value: cell line

value: not applicable

value: ATCC

value: ENCBS194XCJ at ENCODE; https://www.encodeproject.org/ENCBS194XCJ/


title: MPRA from HepG2 (ENCLB820ISQ)

description:
https://www.encodeproject.org/experiments/ENCSR694VUM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR694VUM
assay title: MPRA
possible controls: ENCSR556IED
encode release date: 2024-04-25
lab: Ryan Tewhey, JAX
library encode accession: ENCLB820ISQ
fragmentation methods: none

value: ENCBS237TZU at ENCODE; https://www.encodeproject.org/ENCBS237TZU/


title: Brain, Paxton limnetic, female social control, trial 19

value: whole brain

value: female social control


title: Brain, Paxton limnetic, conspecific courtship, trial 17


title: MPRA from A549 (ENCLB361TZH)

description:
https://www.encodeproject.org/experiments/ENCSR653QXW/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR653QXW
assay title: MPRA
assembly: hg19, GRCh38
possible controls: ENCSR482UPX
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB361TZH
fragmentation methods: none

value: male

value: adult

value: 58 years

value: Ryan Tewhey, JAX

value: ENCBS453CPN at ENCODE; https://www.encodeproject.org/ENCBS453CPN/


title: Brain, Paxton benthic, heterospecific courtship, trial 14

value: Paxton benthic


title: Brain, Priest limnetic, conspecific courtship, trial 15

value: female


title: MPRA from A549 (ENCLB564URV)

description:
https://www.encodeproject.org/experiments/ENCSR653QXW/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR653QXW
assay title: MPRA
assembly: hg19, GRCh38
possible controls: ENCSR482UPX
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB564URV
fragmentation methods: none

value: ENCBS935WAF at ENCODE; https://www.encodeproject.org/ENCBS935WAF/


title: MPRA from A549 (ENCLB589FCW)

description:
https://www.encodeproject.org/experiments/ENCSR653QXW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR653QXW
assay title: MPRA
assembly: hg19, GRCh38
possible controls: ENCSR482UPX
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB589FCW
fragmentation methods: none

value: ENCBS035CVU at ENCODE; https://www.encodeproject.org/ENCBS035CVU/


title: Brain, Priest limnetic, heterospecific courtship, trial 13

value: Priest limnetic

value: heterospecific courtship


title: Brain, Paxton limnetic, conspecific courtship, trial 10

value: Paxton limnetic

value: conspecific courtship


title: MPRA from A549 (ENCLB973ZPT)

description:
https://www.encodeproject.org/experiments/ENCSR653QXW/
***************
biological replicate number: 5
technical replicate number: 1
description:
experiment encode accession: ENCSR653QXW
assay title: MPRA
assembly: hg19, GRCh38
possible controls: ENCSR482UPX
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB973ZPT
fragmentation methods: none

value: cell line

value: not applicable

value: ATCC

value: ENCBS878AYH at ENCODE; https://www.encodeproject.org/ENCBS878AYH/


title: Brain, Priest limnetic, conspecific courtship, trial 9

value: whole brain


title: MPRA from K562 (ENCLB766IZO)

description:
https://www.encodeproject.org/experiments/ENCSR653LWA/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR653LWA
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB766IZO
fragmentation methods: none

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 years

value: ENCBS420RGN at ENCODE; https://www.encodeproject.org/ENCBS420RGN/


title: MPRA from K562 (ENCLB291JHA)

description:
https://www.encodeproject.org/experiments/ENCSR653LWA/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR653LWA
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB291JHA
fragmentation methods: none

value: Ryan Tewhey, JAX

value: ENCBS578HNW at ENCODE; https://www.encodeproject.org/ENCBS578HNW/


title: MPRA from K562 (ENCLB026ZMW)

description:
https://www.encodeproject.org/experiments/ENCSR653LWA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR653LWA
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB026ZMW
fragmentation methods: none

value: female

value: ENCBS383JUN at ENCODE; https://www.encodeproject.org/ENCBS383JUN/


title: Brain, Priest limnetic, conspecific courtship, trial 11

value: Priest limnetic


title: MPRA from A549 (ENCLB320GWV)

description:
https://www.encodeproject.org/experiments/ENCSR645XWQ/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR645XWQ
assay title: MPRA
assembly: hg19, GRCh38
possible controls: ENCSR721WTZ
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB320GWV
fragmentation methods: none

value: male

value: 58 years

value: ENCBS233CQR at ENCODE; https://www.encodeproject.org/ENCBS233CQR/


title: MPRA from HepG2 (ENCLB285PKI)

description:
https://www.encodeproject.org/experiments/ENCSR694VUM/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR694VUM
assay title: MPRA
possible controls: ENCSR556IED
encode release date: 2024-04-25
lab: Ryan Tewhey, JAX
library encode accession: ENCLB285PKI
fragmentation methods: none

value: cell line

value: hepatocellular carcinoma

value: child

value: 15 years

value: ENCBS609RZN at ENCODE; https://www.encodeproject.org/ENCBS609RZN/


title: MPRA from K562 (ENCLB874JMS)

description:
https://www.encodeproject.org/experiments/ENCSR653LWA/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR653LWA
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB874JMS
fragmentation methods: none

value: not applicable

value: chronic myelogenous leukemia (CML)

value: ATCC

value: ENCBS594RPA at ENCODE; https://www.encodeproject.org/ENCBS594RPA/


title: RPMNP, Transformed fallopian tube epithelial cells

city: Shinjuku

first: Tomohiro

last: Tamura

state: Tokyo

address: Shinanomachi 35

department: Department of Extended Intelligence for Medicine, The Ishii-Ishibashi Laboratory

country: Japan

institute: Keio University School of Medicine

data_processing:
The sequencing reads from FASTQ files were trimmed and mapped to the reference mouse genome “GRCm39” and read counts were obtained using CLC Genomics Workbench (Qiagen).
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files including TPM values for each Sample

organism: Mus musculus

extract_protocol:
Cultured organoids were processed for RNA extraction using an RNeasy Plus Mini Kit (Qiagen) according to the manufacturer’s instructions.
The NEBNext Ultra II Directional RNA Library Prep Kit from Illumina (E7760) was used to prepare the sequencing libraries. All libraries were assessed using a TapeStation4200 (Agilent) and quantified using Qubit4.0 (Thermo Fisher Scientific). Multiplexed library pools were sequenced using 50 bp PE reads on a NextSeq2000 platform (Illumina).

tag: cell type

tag: genotype

value: Rb1 KO, Trp53 KO, Myc OE, Nf1 KO, Pten KO

value: Conditioned medium


title: MPRA from K562 (ENCLB920EZZ)

description:
https://www.encodeproject.org/experiments/ENCSR653LWA/
***************
biological replicate number: 5
technical replicate number: 1
description:
experiment encode accession: ENCSR653LWA
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB920EZZ
fragmentation methods: none

tag: line

tag: biosample encode accession

value: female

value: adult

value: 53 years

value: Ryan Tewhey, JAX

value: ENCBS523ZJF at ENCODE; https://www.encodeproject.org/ENCBS523ZJF/


title: MPRA from A549 (ENCLB749DRT)

description:
https://www.encodeproject.org/experiments/ENCSR645XWQ/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR645XWQ
assay title: MPRA
assembly: hg19, GRCh38
possible controls: ENCSR721WTZ
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB749DRT
fragmentation methods: none

tag: collection date

tag: geographic location

value: male

value: 58 years

value: ENCBS293TZX at ENCODE; https://www.encodeproject.org/ENCBS293TZX/


title: cas-nFTE, Normal fallopian tube epithelial cells

source_name: Normal fallopian tube epithelial cells

value: Normal fallopian tube epithelial cells

value: WT


title: soleus myocyte pulldown, mouse 16

type: RNA

city: Columbus

first: George

last: Kyriazis

state: Ohio

address: 460 W 12th Ave

institute: The Ohio State University

description: active RNA immunoprecipitated from left soleus

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials and protocol

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data were processed using Transcriptome Analysis Console 4.0.
Clariom_S_Mouse.r1.pgf
Clariom_S_Mouse.r1.mps

label: biotin

source_name: soleus, left leg

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: not applicable

extract_protocol: Muscles were pulverized in liquid nitrogen, homogenized in polysome buffer and RNA was immunoprecipitated with anti-HA antibody

treatment_protocol: not applicable

value: Myogenin-Cre x RiboTag-Rpl22fl/fl-HA

value: soleus

tag: exercise

value: sedentary


title: casP, Mutated fallopian tube epithelial cells

source_name: Mutated fallopian tube epithelial cells

value: Mutated fallopian tube epithelial cells

value: Trp53 KO


title: MPRA from A549 (ENCLB563IXJ)

description:
https://www.encodeproject.org/experiments/ENCSR645XWQ/
***************
biological replicate number: 5
technical replicate number: 1
description:
experiment encode accession: ENCSR645XWQ
assay title: MPRA
assembly: hg19, GRCh38
possible controls: ENCSR721WTZ
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB563IXJ
fragmentation methods: none

value: cell line

value: not applicable

tag: encode accession

tag: Sex

value: ATCC

value: ENCBS354KYR at ENCODE; https://www.encodeproject.org/ENCBS354KYR/


title: MPRA from A549 (ENCLB104VLJ)

description:
https://www.encodeproject.org/experiments/ENCSR653QXW/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR653QXW
assay title: MPRA
assembly: hg19, GRCh38
possible controls: ENCSR482UPX
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB104VLJ
fragmentation methods: none

tag: dev stage

value: adult

tag: age

value: ENCBS144YUV at ENCODE; https://www.encodeproject.org/ENCBS144YUV/


title: soleus myocyte pulldown, mouse 11


title: MPRA from A549 (ENCLB064DWN)

description:
https://www.encodeproject.org/experiments/ENCSR645XWQ/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR645XWQ
assay title: MPRA
assembly: hg19, GRCh38
possible controls: ENCSR721WTZ
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB064DWN
fragmentation methods: none

tag: passage number

tag: lab

value: Ryan Tewhey, JAX

value: ENCBS605WLU at ENCODE; https://www.encodeproject.org/ENCBS605WLU/


title: RPMP, Transformed fallopian tube epithelial cells

value: Rb1 KO, Trp53 KO, Myc OE, Pten KO

value: Conditioned medium


title: MPRA from GM12878 (ENCLB103QYZ)

description:
https://www.encodeproject.org/experiments/ENCSR645CIP/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR645CIP
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB103QYZ
fragmentation methods: none

source_name: Homo sapiens GM12878 cell line genetically modified (episome) using transient transfection, 24 hours post-nucleic acid delivery time

value: female

tag: health state

value: unknown

tag: source

tag: link

value: ENCBS855ZBP at ENCODE; https://www.encodeproject.org/ENCBS855ZBP/


title: soleus myocyte pulldown, mouse 14

value: Myogenin-Cre x RiboTag-Rpl22fl/fl-HA

tag: tissue

value: soleus


title: nFTE, Normal fallopian tube epithelial cells

tag: cell type

value: Normal fallopian tube epithelial cells

value: WT

tag: treatment


title: RPM, Transformed fallopian tube epithelial cells

tag: genotype

value: Rb1 KO, Trp53 KO, Myc OE


title: MPRA from GM12878 (ENCLB333NYB)

description:
https://www.encodeproject.org/experiments/ENCSR645CIP/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR645CIP
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB333NYB
fragmentation methods: none

tag: line

value: cell line

tag: biosample encode accession

value: not applicable

value: ENCBS752FJJ at ENCODE; https://www.encodeproject.org/ENCBS752FJJ/


title: hi3A

city: wenzhou

first: xiaoyue

last: tao

state: zhejiang

address: puxieshi road, Wenzhou, China

country: China

institute: wenzhou medical university

data_processing:
Briefly, the Fastp software (v0.23.1) was firstly used to perform quality control on the raw data and obtain clean data. Then, the HISAT2 software (v2.1.0) was used to align the obtained clean data referred to the latest reference genome . After that, the Samtools software (v.1.10) was used to sort and convert the SAM files to BAM format, and finally, the Stringtie software (v2.2.1) was used to assemble and quantify the transcripts and genes based on read counts.
Assembly: GCF_000001895.5_Rnor_6.0
Supplementary files format and content: a excel file named "gene_count_matrix.csv" of raw counts  for each sample

organism: Rattus norvegicus

source_name: brain tissue

extract_protocol:
Total RNA  was extracted and purified using a TRIzol reagent (Invitrogen, Carlsbad, CA, USA) for transcriptomic sequencing
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: brain tissue

value: hypoxic-ischemic treatment


title: soleus myocyte pulldown, mouse 3

value: sedentary


title: hi1A


title: soleus myocyte pulldown, mouse 1


title: MPRA from A549 (ENCLB576CMO)

description:
https://www.encodeproject.org/experiments/ENCSR645XWQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR645XWQ
assay title: MPRA
assembly: hg19, GRCh38
possible controls: ENCSR721WTZ
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB576CMO
fragmentation methods: none

tag: collection date

tag: geographic location

value: male

value: adult

value: 58 years

value: Ryan Tewhey, JAX

value: ATCC

value: ENCBS491JYZ at ENCODE; https://www.encodeproject.org/ENCBS491JYZ/


title: MPRA from SK-N-SH (ENCLB643PCR)

description:
https://www.encodeproject.org/experiments/ENCSR623DJZ/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR623DJZ
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB643PCR
fragmentation methods: none

value: SK-N-SH

tag: encode accession

value: female

value: Metastatic neuroblastoma from bone marrow

value: child

value: 4 years

value: ENCBS335ANX at ENCODE; https://www.encodeproject.org/ENCBS335ANX/


title: MPRA from GM12878 (ENCLB184DDG)

description:
https://www.encodeproject.org/experiments/ENCSR645CIP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR645CIP
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB184DDG
fragmentation methods: none

value: cell line

value: not applicable

tag: Sex

value: unknown

value: ENCBS621MLK at ENCODE; https://www.encodeproject.org/ENCBS621MLK/


title: MPRA from GM12878 (ENCLB576XAF)

description:
https://www.encodeproject.org/experiments/ENCSR645CIP/
***************
biological replicate number: 5
technical replicate number: 1
description:
experiment encode accession: ENCSR645CIP
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB576XAF
fragmentation methods: none

tag: dev stage

value: ENCBS298XQY at ENCODE; https://www.encodeproject.org/ENCBS298XQY/


title: hi2A

value: brain tissue

value: hypoxic-ischemic treatment


title: control3A

value: control treatment


title: MPRA from SK-N-SH (ENCLB130GWY)

description:
https://www.encodeproject.org/experiments/ENCSR623DJZ/
***************
biological replicate number: 5
technical replicate number: 1
description:
experiment encode accession: ENCSR623DJZ
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB130GWY
fragmentation methods: none

tag: age

value: Ryan Tewhey, JAX

value: ENCBS955XKE at ENCODE; https://www.encodeproject.org/ENCBS955XKE/


title: RPMN, Transformed fallopian tube epithelial cells

value: Rb1 KO, Trp53 KO, Myc OE, Nf1 KO

value: Conditioned medium


title: control2A


title: MPRA from SK-N-SH (ENCLB643EAA)

description:
https://www.encodeproject.org/experiments/ENCSR623DJZ/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR623DJZ
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB643EAA
fragmentation methods: none

value: SK-N-SH

value: female

tag: passage number

value: ATCC

value: ENCBS559RPA at ENCODE; https://www.encodeproject.org/ENCBS559RPA/


title: control1A


title: MPRA from mammary epithelial cell (ENCLB808DOV)

description:
https://www.encodeproject.org/experiments/ENCSR616NNF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR616NNF
assay title: MPRA
assembly: hg19
possible controls: ENCSR720LEA
encode release date: 2021-09-10
lab: Ryan Tewhey, JAX
library encode accession: ENCLB808DOV
fragmentation methods: none

source_name: Homo sapiens female mammary epithelial primary cell genetically modified (episome) using transient transfection

value: mammary epithelial cell

value: primary cell

tag: lab

value: ENCBS337NZV at ENCODE; https://www.encodeproject.org/ENCBS337NZV/


title: Hypsibius exemplaris Control, replicate 1

city: Tsukuba

first: Yuki

last: Yoshida

state: Ibaraki

address: 1-2 Owashi

department: NIAS

institute: NARO

data_processing:
The quality of RNA-Seq reads were validated with FastQC v0.11.3
The sequenced reads were mapped to CDS and quantified with RSEM v1.2.26 {Li, 2011 #3027} and bowtie2 v2.2.9 {Langmead, 2012 #233} using the Trinity align_and_estimate_abundance.pl utility {Grabherr, 2011 #312}. Differential expression was tested with DESeq2 v1.22.2 {Love, 2014 #870} using the Trinity run_DE_analysis.pl, and transcripts with adjusted p-values below 0.05 and fold change over 1.5 or below 2/3 were designated as differentially expressed genes.
Genome_build: GCA_002082055.1_nHd_3.1
Supplementary_files_format_and_content: RSEM quantified TPM values

organism: Hypsibius exemplaris

source_name: Hypsibius exemplaris Control

growth_protocol: H. exemplaris was cultured following our previous studies. Briefly, specimens were placed on 2% agar gels using Volvic water, supplied with Volvic water containing Chlorella vulgaris. Individuals were collected and moved to a new agar plate every 7 days.

extract_protocol:
Frozen samples were submitted to transcriptome sequencing (N=3). The total RNA was extracted with Direct-Zol Micro Kit and quantified with Qubit RNA HS.
An Illumina sequencing library was constructed from 30ng of total RNA with NEB Next Ultra RNA following the manufacture’s protocol.

treatment_protocol: Fifty individuals per sample were placed in 96 well flat bottom plates and was exposed to 200µL 100µM Bleomycin (melted in Volvic water) for 24 hours (N=5). A control series exposed to Volvic water was also set. After 24 hours, the control specimens and T0 specimens were collected and placed in a microtube with the least amount of water possible and frozen at -80˚C. The remining samples were washed with 300µL Volvic water twice to remove bleomycin and were placed on 45mm agar plates with 2mL volvic water supplied with 10µL Chlorella to feed on. These specimens were incubated at 18˚C until sampling. After 1,3, 6, 9, 12, 24 hours, each sample were collected as stated above and frozen at -80˚C.

value: Control

tag: time

value: Whole body


title: MPRA from SK-N-SH (ENCLB558UHQ)

description:
https://www.encodeproject.org/experiments/ENCSR623DJZ/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR623DJZ
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB558UHQ
fragmentation methods: none

value: cell line

value: not applicable

tag: health state

value: Metastatic neuroblastoma from bone marrow

value: child

value: 4 years

tag: source

value: ENCBS345SMA at ENCODE; https://www.encodeproject.org/ENCBS345SMA/


title: MPRA from SK-N-SH (ENCLB830RGG)

description:
https://www.encodeproject.org/experiments/ENCSR623DJZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR623DJZ
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB830RGG
fragmentation methods: none

value: Ryan Tewhey, JAX

tag: link

value: ENCBS772RDT at ENCODE; https://www.encodeproject.org/ENCBS772RDT/


title: Hypsibius exemplaris Control, replicate 3

tag: tissue


title: Hypsibius exemplaris Control, replicate 2

tag: treatment


title: MPRA from GM12878 (ENCLB318OSR)

description:
https://www.encodeproject.org/experiments/ENCSR645CIP/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR645CIP
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB318OSR
fragmentation methods: none

value: unknown

value: adult

value: ENCBS348WMC at ENCODE; https://www.encodeproject.org/ENCBS348WMC/


title: Hypsibius exemplaris 12h hours after exposure to 100µM BML, replicate 3

value: BML

value: 12h hours


title: MPRA from GM12878 (ENCLB265UAD)

description:
https://www.encodeproject.org/experiments/ENCSR587IBO/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR587IBO
assay title: MPRA
possible controls: ENCSR441MQR
encode release date: 2024-04-25
lab: Ryan Tewhey, JAX
library encode accession: ENCLB265UAD
fragmentation methods: none

value: female

value: Coriell

value: ENCBS476LPY at ENCODE; https://www.encodeproject.org/ENCBS476LPY/


title: Hypsibius exemplaris 12h hours after exposure to 100µM BML, replicate 2

value: Whole body


title: MPRA from mammary epithelial cell (ENCLB519BUM)

description:
https://www.encodeproject.org/experiments/ENCSR616NNF/
***************
biological replicate number: 5
technical replicate number: 1
description:
experiment encode accession: ENCSR616NNF
assay title: MPRA
assembly: hg19
possible controls: ENCSR720LEA
encode release date: 2021-09-10
lab: Ryan Tewhey, JAX
library encode accession: ENCLB519BUM
fragmentation methods: none

value: mammary epithelial cell

value: primary cell

value: ATCC

value: ENCBS358NGU at ENCODE; https://www.encodeproject.org/ENCBS358NGU/


title: Hypsibius exemplaris 24h hours after exposure to 100µM BML, replicate 3

value: 24h hours


title: MPRA from GM12878 (ENCLB686VFY)

description:
https://www.encodeproject.org/experiments/ENCSR587IBO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR587IBO
assay title: MPRA
possible controls: ENCSR441MQR
encode release date: 2024-04-25
lab: Ryan Tewhey, JAX
library encode accession: ENCLB686VFY
fragmentation methods: none

value: cell line

value: not applicable

value: ENCBS302NIH at ENCODE; https://www.encodeproject.org/ENCBS302NIH/


title: Hypsibius exemplaris 24h hours after exposure to 100µM BML, replicate 2


title: MPRA from mammary epithelial cell (ENCLB484CYS)

description:
https://www.encodeproject.org/experiments/ENCSR616NNF/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR616NNF
assay title: MPRA
assembly: hg19
possible controls: ENCSR720LEA
encode release date: 2021-09-10
lab: Ryan Tewhey, JAX
library encode accession: ENCLB484CYS
fragmentation methods: none

value: unknown

value: Ryan Tewhey, JAX

value: ENCBS769PDL at ENCODE; https://www.encodeproject.org/ENCBS769PDL/


title: MPRA from mammary epithelial cell (ENCLB593YJD)

description:
https://www.encodeproject.org/experiments/ENCSR616NNF/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR616NNF
assay title: MPRA
assembly: hg19
possible controls: ENCSR720LEA
encode release date: 2021-09-10
lab: Ryan Tewhey, JAX
library encode accession: ENCLB593YJD
fragmentation methods: none

value: ENCBS284KWE at ENCODE; https://www.encodeproject.org/ENCBS284KWE/


title: Hypsibius exemplaris 12h hours after exposure to 100µM BML, replicate 1

value: BML

value: 12h hours


title: MPRA from GM12878 (ENCLB450UGQ)

description:
https://www.encodeproject.org/experiments/ENCSR587IBO/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR587IBO
assay title: MPRA
possible controls: ENCSR441MQR
encode release date: 2024-04-25
lab: Ryan Tewhey, JAX
library encode accession: ENCLB450UGQ
fragmentation methods: none

value: female

value: adult

value: Coriell

value: ENCBS572SWY at ENCODE; https://www.encodeproject.org/ENCBS572SWY/


title: Hypsibius exemplaris 24h hours after exposure to 100µM BML, replicate 1

value: Whole body


title: Hypsibius exemplaris 09h hours after exposure to 100µM BML, replicate 1

value: 09h hours


title: MPRA from SK-N-SH (ENCLB365VDG)

description:
https://www.encodeproject.org/experiments/ENCSR579QGV/
***************
biological replicate number: 5
technical replicate number: 1
description:
experiment encode accession: ENCSR579QGV
assay title: MPRA
assembly: hg19, GRCh38
possible controls: ENCSR691FFI
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB365VDG
fragmentation methods: none

value: SK-N-SH

value: Metastatic neuroblastoma from bone marrow

value: child

value: 4 years

value: ATCC

value: ENCBS475YUR at ENCODE; https://www.encodeproject.org/ENCBS475YUR/


title: MPRA from GM12878 (ENCLB692PTX)

description:
https://www.encodeproject.org/experiments/ENCSR587IBO/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR587IBO
assay title: MPRA
possible controls: ENCSR441MQR
encode release date: 2024-04-25
lab: Ryan Tewhey, JAX
library encode accession: ENCLB692PTX
fragmentation methods: none

value: cell line

value: not applicable

value: unknown

value: Ryan Tewhey, JAX

value: ENCBS456ERH at ENCODE; https://www.encodeproject.org/ENCBS456ERH/


title: MPRA from SK-N-SH (ENCLB388IEO)

description:
https://www.encodeproject.org/experiments/ENCSR579QGV/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR579QGV
assay title: MPRA
assembly: hg19, GRCh38
possible controls: ENCSR691FFI
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB388IEO
fragmentation methods: none

value: female

value: ENCBS672DWR at ENCODE; https://www.encodeproject.org/ENCBS672DWR/


title: Hypsibius exemplaris 09h hours after exposure to 100µM BML, replicate 3

value: BML


title: MPRA from GM12878 (ENCLB525GKO)

description:
https://www.encodeproject.org/experiments/ENCSR587IBO/
***************
biological replicate number: 5
technical replicate number: 1
description:
experiment encode accession: ENCSR587IBO
assay title: MPRA
possible controls: ENCSR441MQR
encode release date: 2024-04-25
lab: Ryan Tewhey, JAX
library encode accession: ENCLB525GKO
fragmentation methods: none

value: adult

value: Coriell

value: ENCBS315UJQ at ENCODE; https://www.encodeproject.org/ENCBS315UJQ/


title: Hypsibius exemplaris 06h hours after exposure to 100µM BML, replicate 2

value: 06h hours

value: Whole body


title: MPRA from mammary epithelial cell (ENCLB557WGX)

description:
https://www.encodeproject.org/experiments/ENCSR616NNF/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR616NNF
assay title: MPRA
assembly: hg19
possible controls: ENCSR720LEA
encode release date: 2021-09-10
lab: Ryan Tewhey, JAX
library encode accession: ENCLB557WGX
fragmentation methods: none

value: mammary epithelial cell

value: primary cell

value: ENCBS438VCP at ENCODE; https://www.encodeproject.org/ENCBS438VCP/


title: Hypsibius exemplaris 06h hours after exposure to 100µM BML, replicate 3


title: Hypsibius exemplaris 09h hours after exposure to 100µM BML, replicate 2

value: 09h hours


title: MPRA from SK-N-SH (ENCLB077YDZ)

description:
https://www.encodeproject.org/experiments/ENCSR579QGV/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR579QGV
assay title: MPRA
assembly: hg19, GRCh38
possible controls: ENCSR691FFI
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB077YDZ
fragmentation methods: none

value: SK-N-SH

value: cell line

value: Metastatic neuroblastoma from bone marrow

value: child

value: 4 years

value: ATCC

value: ENCBS470WDQ at ENCODE; https://www.encodeproject.org/ENCBS470WDQ/


title: Hypsibius exemplaris 06h hours after exposure to 100µM BML, replicate 1

value: BML


title: MPRA from SK-N-SH (ENCLB197CMI)

description:
https://www.encodeproject.org/experiments/ENCSR579QGV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR579QGV
assay title: MPRA
assembly: hg19, GRCh38
possible controls: ENCSR691FFI
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB197CMI
fragmentation methods: none

value: not applicable

value: female

value: Ryan Tewhey, JAX

value: ENCBS514NWD at ENCODE; https://www.encodeproject.org/ENCBS514NWD/


title: MPRA from SK-N-SH (ENCLB000PPE)

description:
https://www.encodeproject.org/experiments/ENCSR579QGV/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR579QGV
assay title: MPRA
assembly: hg19, GRCh38
possible controls: ENCSR691FFI
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB000PPE
fragmentation methods: none

value: ENCBS085STF at ENCODE; https://www.encodeproject.org/ENCBS085STF/


title: Hypsibius exemplaris 03h hours after exposure to 100µM BML, replicate 1

value: 03h hours

value: Whole body


title: MPRA from SK-N-SH (ENCLB233PSM)

description:
https://www.encodeproject.org/experiments/ENCSR574GPT/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR574GPT
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB233PSM
fragmentation methods: none

value: ENCBS770KHG at ENCODE; https://www.encodeproject.org/ENCBS770KHG/


title: MPRA from SK-N-SH (ENCLB066HFW)

description:
https://www.encodeproject.org/experiments/ENCSR574GPT/
***************
biological replicate number: 5
technical replicate number: 1
description:
experiment encode accession: ENCSR574GPT
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB066HFW
fragmentation methods: none

value: ENCBS717IWA at ENCODE; https://www.encodeproject.org/ENCBS717IWA/


title: Hypsibius exemplaris 01h hours after exposure to 100µM BML, replicate 3

value: 01h hours


title: Hypsibius exemplaris 01h hours after exposure to 100µM BML, replicate 2


title: MPRA from SK-N-SH (ENCLB896WXE)

description:
https://www.encodeproject.org/experiments/ENCSR574GPT/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR574GPT
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB896WXE
fragmentation methods: none

value: SK-N-SH

value: cell line

value: ENCBS772HSN at ENCODE; https://www.encodeproject.org/ENCBS772HSN/


title: Hypsibius exemplaris 01h hours after exposure to 100µM BML, replicate 1


title: MPRA from SK-N-SH (ENCLB706QAD)

description:
https://www.encodeproject.org/experiments/ENCSR574GPT/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR574GPT
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB706QAD
fragmentation methods: none

value: Metastatic neuroblastoma from bone marrow

value: child

value: 4 years

value: ENCBS184DCH at ENCODE; https://www.encodeproject.org/ENCBS184DCH/


title: Hypsibius exemplaris 00h hours after exposure to 100µM BML, replicate 3

value: BML

value: 00h hours


title: MPRA from SK-N-SH (ENCLB841BST)

description:
https://www.encodeproject.org/experiments/ENCSR563TTU/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR563TTU
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB841BST
fragmentation methods: none

value: not applicable

value: female

value: Ryan Tewhey, JAX

value: ATCC

value: ENCBS337FFL at ENCODE; https://www.encodeproject.org/ENCBS337FFL/


title: MPRA from SK-N-SH (ENCLB651HEG)

description:
https://www.encodeproject.org/experiments/ENCSR574GPT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR574GPT
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB651HEG
fragmentation methods: none

value: ENCBS776DAR at ENCODE; https://www.encodeproject.org/ENCBS776DAR/


title: Hypsibius exemplaris 03h hours after exposure to 100µM BML, replicate 3

value: 03h hours

value: Whole body


title: Hypsibius exemplaris 03h hours after exposure to 100µM BML, replicate 2


title: Hypsibius exemplaris 00h hours after exposure to 100µM BML, replicate 1


title: MPRA from SK-N-SH (ENCLB104CNF)

description:
https://www.encodeproject.org/experiments/ENCSR563TTU/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR563TTU
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB104CNF
fragmentation methods: none

value: SK-N-SH

value: ENCBS939QDE at ENCODE; https://www.encodeproject.org/ENCBS939QDE/


title: MPRA from SK-N-SH (ENCLB559TLT)

description:
https://www.encodeproject.org/experiments/ENCSR563TTU/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR563TTU
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB559TLT
fragmentation methods: none

value: cell line

value: ENCBS832RJO at ENCODE; https://www.encodeproject.org/ENCBS832RJO/


title: MPRA from SK-N-SH (ENCLB626IVI)

description:
https://www.encodeproject.org/experiments/ENCSR563TTU/
***************
biological replicate number: 5
technical replicate number: 1
description:
experiment encode accession: ENCSR563TTU
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB626IVI
fragmentation methods: none

value: Metastatic neuroblastoma from bone marrow

value: child

value: ENCBS827XRK at ENCODE; https://www.encodeproject.org/ENCBS827XRK/


title: MPRA from SK-N-SH (ENCLB167SVL)

description:
https://www.encodeproject.org/experiments/ENCSR563TTU/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR563TTU
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB167SVL
fragmentation methods: none

value: 4 years

value: ENCBS137THQ at ENCODE; https://www.encodeproject.org/ENCBS137THQ/


title: dTAG_8hr_Replicate2

city: Dallas

first: Ivan

last: D'Orso

state: TX

address: 5323 Harry Hines

department: Microbiology

institute: UT Southwestern Medical Center

data_processing:
Raw fastq data files were ran through fastqc/0.11.8 and low quality reads/adapter contamination were removed using trimgalore/0.6.4.
Reads were mapped to the hg38 human reference genome and ERCC RNA spike-in mix using star/2.7.3a.
featureCounts (subread/1.6.3) was used to calculate counts across the entire gene of protein coding genes using a .gtf file containing all protein coding genes and ERCC RNA spike-in mix.
EDASeq/2.32.0, RUVSeq/1.32.0, and EdgeR/3.40.1 commands were used for RNA spike-in normalization and differential gene expression analysis of genes that contained at least 10 counts in 6 samples.
Assembly: hg38
Supplementary files format and content: comma-separated txt file with read counts for all features

molecule: nuclear RNA

growth_protocol: All cell lines were maintained in DMEM supplemented with 7% fetal bovine serum (FBS) and antibiotics (Pen/Strep) in humidified atmosphere with 5% CO2 at 37C. For treatments, cells were treated with either DMSO (vehicle control) or dTAG for 8 hr to induce KAP1 depletion.

extract_protocol:
For TT-Seq, the protocol from Patrick Cramer’s lab was followed with minor modifications. Three 10 cm tissue culture dishes per condition were seeded such that cells reached 75% confluence 3-days post seeding. On the third day, cells were treated with DMSO or dTAG for 8 hr, after which 500 μM 4-Thiouridine (Sigma, catalog T4509-25MG) was added to the media for 10 min. An extra dish was seeded per condition and ~12E6 cells were counted per plate and thus 36E6 cells/sample were used to prepare RNA. Cells were washed with 5 mL of 1X PBS once and then immediately 1 mL of TRIzol™ Reagent (Thermo, catalog 15596026) was added and followed by 10 min of rocking.
KAPA RNA Hyper+RiboErase HMR kit was used (Roche, catalog 8098131702) following manufacturers instructions.

tag: cell line

tag: genotype


title: dTAG_8hr_Serum_0_30_Replicate3

data_processing:
Raw fastq data files for were ran through fastqc/0.11.8 and low quality reads/adapter contamination were removed using trimgalore/0.6.4.
Reads were mapped to the hg38 human reference genome and ERCC RNA spike-in mix using star/2.7.3a.
featureCounts (subread/1.6.3) was used to calculate counts across the entire gene of protein coding genes using a .gtf file containing all protein coding genes ans ERCC RNA spike-ins.
EDASeq/2.32.0, RUVSeq/1.32.0, and EdgeR/3.40.1 commands were used for spike-in normalization and differential gene expression analysis of genes that contained at least 10 counts in 6 samples.
Assembly: hg38
Supplementary files format and content: comma-separated txt file with read counts for all features

growth_protocol: All cell lines were maintained in DMEM supplemented with 7% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C. For treatments, cells were placed in serum-free media for 48 hr prior to serum treatment for the corresponding time point. 8 hr prior to serum treatment, cells were treated with DMSO or dTAG to induce KAP1 depletion or control.

extract_protocol:
Cells were treated as described and RNA was extracted using the Zymo Quick-RNA MiniPrep Kit (Zymo Research, catalog R1055) following the kit instructions.
KAPA RNA Hyper+RiboErase HMR kit was used (Roche, catalog 8098131702) following manufacturers instructions.


title: DMSO_8hr_Replicate2


title: dTAG_8hr_Replicate1


title: DMSO_8hr_Replicate1


title: MPRA from SK-N-SH (ENCLB080MXA)

description:
https://www.encodeproject.org/experiments/ENCSR562GGR/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR562GGR
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB080MXA
fragmentation methods: none

tag: line

tag: biosample encode accession

value: not applicable

value: ENCBS137RCP at ENCODE; https://www.encodeproject.org/ENCBS137RCP/


title: dTAG_8hr_Serum_0_30_Replicate1


title: MPRA from SK-N-SH (ENCLB554EST)

description:
https://www.encodeproject.org/experiments/ENCSR562GGR/
***************
biological replicate number: 5
technical replicate number: 1
description:
experiment encode accession: ENCSR562GGR
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB554EST
fragmentation methods: none

tag: collection date

tag: geographic location

value: female

value: Ryan Tewhey, JAX

value: ENCBS567QWH at ENCODE; https://www.encodeproject.org/ENCBS567QWH/


title: MPRA from SK-N-SH (ENCLB379RWZ)

description:
https://www.encodeproject.org/experiments/ENCSR562GGR/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR562GGR
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB379RWZ
fragmentation methods: none

tag: encode accession

tag: Sex

value: ATCC

value: ENCBS017IMU at ENCODE; https://www.encodeproject.org/ENCBS017IMU/


title: dTAG_8hr_Serum_30_Replicate3


title: dTAG_8hr_Serum_0_30_Replicate2


title: MPRA from GM12878 (ENCLB921ZBR)

description:
https://www.encodeproject.org/experiments/ENCSR560QIE/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR560QIE
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB921ZBR
fragmentation methods: none

value: unknown

tag: dev stage

value: adult

tag: age

value: ENCBS197OKI at ENCODE; https://www.encodeproject.org/ENCBS197OKI/


title: MPRA from SK-N-SH (ENCLB154ZLU)

description:
https://www.encodeproject.org/experiments/ENCSR562GGR/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR562GGR
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB154ZLU
fragmentation methods: none

value: SK-N-SH

value: cell line

tag: passage number

tag: lab

value: ENCBS962PVL at ENCODE; https://www.encodeproject.org/ENCBS962PVL/


title: dTAG_8hr_Serum_30_Replicate1


title: MPRA from GM12878 (ENCLB708LEN)

description:
https://www.encodeproject.org/experiments/ENCSR560QIE/
***************
biological replicate number: 5
technical replicate number: 1
description:
experiment encode accession: ENCSR560QIE
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB708LEN
fragmentation methods: none

tag: health state

value: ENCBS841JKX at ENCODE; https://www.encodeproject.org/ENCBS841JKX/


title: DMSO_8hr_Serum_0_30_Replicate3


title: dTAG_8hr_Serum_30_Replicate2


title: Hypsibius exemplaris 00h hours after exposure to 100µM BML, replicate 2

value: BML

tag: time

value: 00h hours

value: Whole body


title: MPRA from GM12878 (ENCLB173XFW)

description:
https://www.encodeproject.org/experiments/ENCSR560QIE/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR560QIE
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB173XFW
fragmentation methods: none

value: not applicable

tag: source

tag: link

value: ENCBS171ZBZ at ENCODE; https://www.encodeproject.org/ENCBS171ZBZ/


title: DMSO_8hr_Serum_0_30_Replicate2


title: MPRA from GM12878 (ENCLB724ELM)

description:
https://www.encodeproject.org/experiments/ENCSR560QIE/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR560QIE
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB724ELM
fragmentation methods: none

value: female

value: ENCBS622KPZ at ENCODE; https://www.encodeproject.org/ENCBS622KPZ/


title: DMSO_8hr_Serum_0_30_Replicate1


title: MPRA from GM12878 (ENCLB978JSQ)

description:
https://www.encodeproject.org/experiments/ENCSR560QIE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR560QIE
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB978JSQ
fragmentation methods: none

value: Ryan Tewhey, JAX

value: ENCBS788FHJ at ENCODE; https://www.encodeproject.org/ENCBS788FHJ/


title: MPRA from HepG2 (ENCLB613PJA)

description:
https://www.encodeproject.org/experiments/ENCSR554UKK/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR554UKK
assay title: MPRA
assembly: hg19, GRCh38
possible controls: ENCSR836ULU
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB613PJA
fragmentation methods: none

value: male

value: hepatocellular carcinoma

value: child

value: 15 years

value: ATCC

value: ENCBS819WPM at ENCODE; https://www.encodeproject.org/ENCBS819WPM/


title: DMSO_8hr_Serum_30_Replicate3


title: MPRA from SK-N-SH (ENCLB004SBR)

description:
https://www.encodeproject.org/experiments/ENCSR562GGR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR562GGR
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB004SBR
fragmentation methods: none

value: SK-N-SH

value: cell line

value: Metastatic neuroblastoma from bone marrow

value: 4 years

value: ENCBS820GMQ at ENCODE; https://www.encodeproject.org/ENCBS820GMQ/


title: MPRA from HepG2 (ENCLB616TOO)

description:
https://www.encodeproject.org/experiments/ENCSR554UKK/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR554UKK
assay title: MPRA
assembly: hg19, GRCh38
possible controls: ENCSR836ULU
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB616TOO
fragmentation methods: none

value: not applicable

value: ENCBS813WBR at ENCODE; https://www.encodeproject.org/ENCBS813WBR/


title: DMSO_8hr_Serum_30_Replicate1


title: MPRA from HepG2 (ENCLB915QVN)

description:
https://www.encodeproject.org/experiments/ENCSR554UKK/
***************
biological replicate number: 5
technical replicate number: 1
description:
experiment encode accession: ENCSR554UKK
assay title: MPRA
assembly: hg19, GRCh38
possible controls: ENCSR836ULU
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB915QVN
fragmentation methods: none

value: ENCBS933IJC at ENCODE; https://www.encodeproject.org/ENCBS933IJC/


title: DMSO_8hr_Serum_30_Replicate2


title: PRO_dTAG_Serum5_Replicate1

data_processing:
The PRO-seq reads were quality-checked through fastqc/0.11.8 and adapters removed by Cutadapt/2.5.
Trimmed reads were aligned to the hg38 human reference genome using BWA/0.7.5.
Mapped reads were sorted and captured in bam files for further downstream analysis and bigwig files were generated using deeptools.
Assembly: hg38
Supplementary files format and content: BigWig
Library strategy: PRO-Seq

growth_protocol: All cell lines were maintained in DMEM supplemented with 7% fetal bovine serum (FBS) and antibiotics (Pen/Strep) in humidified atmosphere with 5% CO2 at 37C. For treatments, cells were placed in serum-free media for 48 hr prior to serum treatment for the corresponding time point. 8 hr prior to serum treatment, cells were treated with DMSO or dTAG to induce KAP1 depletion or control.

extract_protocol:
Cells were processed for PRO-Seq by washing and permeabilization as described in the methods of the manuscript. The qPRO-Seq protocol was followed with minor modifications (Judd et al. 2020). Cells were seeded in 10 cm tissue culture dishes, treated as indicated and were ~90% confluent prior to collection. For each PRO-Seq, ~4E6 cells were utilized. To prepare permeabilized cells for run-on, cells were first washed twice on the plate with 5 mL of ice-cold 1X PBS. Then, 2.5 mL of ice-cold Cell Permeabilization Buffer (CPB) (10 mM Tris-Cl pH = 8.0 , 250 mM Sucrose, 10 mM KCl, 5 mM MgCl2, 1 mM EGTA pH = 8.0, 0.1% NP-40, 0.5 mM DTT, 0.05% Tween-20, 0.1% Triton X-100, 10% Glycerol, 1X protease inhibitor, and 2 µL SUPERase-In RNase inhibitor (Thermo, catalog AM2696) per 10 mL was immediately added to the tissue culture dish. Triton X-100 was added to CPB to increase permeabilization percent. Dishes were placed on ice and then immediately scraped with a cell scraper. At this point, cells were collected in a 15 mL tube, placed on ice for 5 min, checked for permeabilization by trypan blue staining (>95%), and then centrifuged in a swinging bucket rotor (1000xg, 4 min, 4°C). Following this, cells were handled using cut tips. The supernatant was removed and samples were resuspended in 1 mL of Cell Wash Buffer (CWB) (10 mM Tris-Cl pH = 8.0, 250 mM Sucrose, 10 mM KCl, 5 mM MgCl2, 1 mM EGTA pH = 8.0, 0.5 mM DTT, 10% Glycerol, 1X protease inhibitor, and 2 µL SUPERase-In RNase inhibitor per 10 mL) and centrifuged (1000xg, 4 min, 4°C) for a total of 2 washes. After the second wash, samples were resuspended in 1 mL total Cell Freeze Buffer (CFB) (50 mM Tris-Cl pH = 8.0, 5 mM MgCl2, 0.5 mM DTT, 40% Glycerol, 1.1 mM EDTA pH = 8.0, and 2 µL SUPERase-In RNase inhibitor per 10 mL), counted by hemacytometer, and then spun down in 1.5 mL tubes in an angled rotor centrifuge (1000xg, 5 min, 4°C). Samples were resuspended in 52 μL of CFB for every 4E6 cells, flash frozen in liquid nitrogen, and then frozen at -80°C until ready to use.
Library was prepared with individual reagents following the protocol from Judd et al (dx.doi.org/10.17504/protocols.io.57dg9i6) exactly as described.


title: PRO_dTAG_Serum10_Replicate2


title: PRO_dTAG_Serum5_Replicate2


title: MPRA from HepG2 (ENCLB219CLD)

description:
https://www.encodeproject.org/experiments/ENCSR554UKK/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR554UKK
assay title: MPRA
assembly: hg19, GRCh38
possible controls: ENCSR836ULU
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB219CLD
fragmentation methods: none

value: ENCBS025BOP at ENCODE; https://www.encodeproject.org/ENCBS025BOP/


title: MPRA from A549 (ENCLB979PXS)

description:
https://www.encodeproject.org/experiments/ENCSR523VYM/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR523VYM
assay title: MPRA
assembly: hg19, GRCh38
possible controls: ENCSR845WYW
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB979PXS
fragmentation methods: none

value: adult

value: 58 years

value: Ryan Tewhey, JAX

value: ENCBS624ISU at ENCODE; https://www.encodeproject.org/ENCBS624ISU/


title: PRO_dTAG_Serum10_Replicate1


title: MPRA from A549 (ENCLB830MAH)

description:
https://www.encodeproject.org/experiments/ENCSR523VYM/
***************
biological replicate number: 5
technical replicate number: 1
description:
experiment encode accession: ENCSR523VYM
assay title: MPRA
assembly: hg19, GRCh38
possible controls: ENCSR845WYW
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB830MAH
fragmentation methods: none

value: male

value: ENCBS385CXH at ENCODE; https://www.encodeproject.org/ENCBS385CXH/


title: PRO_dTAG_Serum0_Replicate2


title: MPRA from A549 (ENCLB185IHJ)

description:
https://www.encodeproject.org/experiments/ENCSR523VYM/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR523VYM
assay title: MPRA
assembly: hg19, GRCh38
possible controls: ENCSR845WYW
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB185IHJ
fragmentation methods: none

value: ATCC

value: ENCBS078LNY at ENCODE; https://www.encodeproject.org/ENCBS078LNY/


title: MPRA from HepG2 (ENCLB547MIA)

description:
https://www.encodeproject.org/experiments/ENCSR554UKK/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR554UKK
assay title: MPRA
assembly: hg19, GRCh38
possible controls: ENCSR836ULU
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB547MIA
fragmentation methods: none

value: hepatocellular carcinoma

value: child

value: 15 years

value: ENCBS380POW at ENCODE; https://www.encodeproject.org/ENCBS380POW/


title: MPRA from A549 (ENCLB377YUL)

description:
https://www.encodeproject.org/experiments/ENCSR523VYM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR523VYM
assay title: MPRA
assembly: hg19, GRCh38
possible controls: ENCSR845WYW
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB377YUL
fragmentation methods: none

value: cell line

value: ENCBS248IIH at ENCODE; https://www.encodeproject.org/ENCBS248IIH/


title: MPRA from A549 (ENCLB248YCM)

description:
https://www.encodeproject.org/experiments/ENCSR523VYM/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR523VYM
assay title: MPRA
assembly: hg19, GRCh38
possible controls: ENCSR845WYW
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB248YCM
fragmentation methods: none

value: not applicable

value: ENCBS809LFS at ENCODE; https://www.encodeproject.org/ENCBS809LFS/


title: PRO_DMSO_Serum5_Replicate2


title: MPRA from SK-N-SH (ENCLB223RNV)

description:
https://www.encodeproject.org/experiments/ENCSR505LQA/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR505LQA
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB223RNV
fragmentation methods: none

value: SK-N-SH

value: female

value: Metastatic neuroblastoma from bone marrow

value: 4 years

value: ENCBS306TNS at ENCODE; https://www.encodeproject.org/ENCBS306TNS/


title: PRO_DMSO_Serum5_Replicate1


title: PRO_DMSO_Serum10_Replicate2


title: MPRA from SK-N-SH (ENCLB295EHY)

description:
https://www.encodeproject.org/experiments/ENCSR505LQA/
***************
biological replicate number: 5
technical replicate number: 1
description:
experiment encode accession: ENCSR505LQA
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB295EHY
fragmentation methods: none

value: Ryan Tewhey, JAX

value: ENCBS168IKZ at ENCODE; https://www.encodeproject.org/ENCBS168IKZ/


title: MPRA from SK-N-SH (ENCLB849OMB)

description:
https://www.encodeproject.org/experiments/ENCSR505LQA/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR505LQA
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB849OMB
fragmentation methods: none

value: ATCC

value: ENCBS380CHL at ENCODE; https://www.encodeproject.org/ENCBS380CHL/


title: PRO_DMSO_Serum0_Replicate2


title: MPRA from SK-N-SH (ENCLB286ZEW)

description:
https://www.encodeproject.org/experiments/ENCSR505LQA/
***************
biological replicate number: 6
technical replicate number: 1
description:
experiment encode accession: ENCSR505LQA
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB286ZEW
fragmentation methods: none

value: ENCBS212DFY at ENCODE; https://www.encodeproject.org/ENCBS212DFY/


title: MPRA from SK-N-SH (ENCLB608ANE)

description:
https://www.encodeproject.org/experiments/ENCSR505LQA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR505LQA
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB608ANE
fragmentation methods: none

value: child

value: ENCBS286BGW at ENCODE; https://www.encodeproject.org/ENCBS286BGW/


title: MPRA from HEK293 (ENCLB693DVL)

description:
https://www.encodeproject.org/experiments/ENCSR481QRH/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR481QRH
assay title: MPRA
assembly: hg19
possible controls: ENCSR332LAV
encode release date: 2021-09-10
lab: Ryan Tewhey, JAX
library encode accession: ENCLB693DVL
fragmentation methods: none

source_name: Homo sapiens HEK293 cell line genetically modified (episome) using transient transfection

value: unknown

value: embryonic

value: ENCBS561NAZ at ENCODE; https://www.encodeproject.org/ENCBS561NAZ/


title: PRO_DMSO_Serum0_Replicate1


title: pSPT5_Thr806P_dTAG_Serum5

library_source: genomic

data_processing:
raw fastq data files were ran through fastqc/0.11.8 and low quality reads/adapter contamination were removed using trimgalore/0.6.4
Reads were mapped to the hg38 human reference genome using bowtie2/2.4.2. Reads were also mapped to the dm6 Drosophila genome to extract reads originating from the spike-ins chromatin for normalization purposes.
Duplicates were marked and removed using picard/2.10.3 and then files were sorted and indexed using samtools/1.6 in preparation for Bigwig generation.
Normalized BigWigs were made from sorted bam files using Deeptools command bamCoverage using either CPM normalization or scale factors generated from sorted Drosophila bam files.
Assembly: hg38
Supplementary files format and content: bigWig

molecule: genomic DNA

growth_protocol: All cell lines were maintained in DMEM supplemented with 7% fetal bovine serum (FBS) and antibiotics (Pen/Strep) in humidified atmosphere with 5% CO2 at 37C. For treatments, cells were placed in serum-free media for 48 hr prior to serum treatment for the corresponding time point. 8 hr prior to serum treatment, cells were pre-incubated with DMSO (vehicle control) or dTAG to induce KAP1 depletion.

extract_protocol:
For each ChIP, 1 x 15-cm tissue culture dish (yielding ~30E6 cells/plate) was utilized and seeded according to the experimental design in each figure (DMSO/dTAG +/- serum at different time points), and 20E6 cells were utilized per ChIP. For all Pol II ChIPs, cells were crosslinked with 0.5% methanol-free formaldehyde (Thermo Fisher Scientific, 28908) by adding directly to the dish in media at room temperature for 10 min with rocking and neutralization with 150 mM glycine for 5 min with rocking. For the ChIPs including HA (KAP1), SPT5, CDK9, TFIIB, MED1, and CDK7, 1% formaldehyde for 10 min was used instead of 0.5%. For all experiments, the media was removed and cells were washed twice with cold 1X PBS, cold PBS was added and then cells were scraped off the plate. Cells were centrifuged (1000xg, 5 min, 4°C), and pelleted, flash frozen in liquid nitrogen, and frozen at -80°C until ready to use. To perform the ChIP, cells were resuspended in 2 mL/dish of Farnham Lysis Buffer (5 mM PIPES pH = 8.0, 85 mM KCl, 0.5% NP-40, 1 mM PMSF, 1X Protease Inhibitor (RPI, catalog P50900-1)), counted by hemacytometer, resuspended to 10E6 cells/mL, nutated for 30 min at 4°C, and then centrifuged to isolate nuclei (1000xg, 5 min, 4°C). The supernatant was removed and nuclei resuspended in Szak’s RIPA Buffer (50 mM Tris-HCl pH = 8.0, 1% NP-40, 150 mM NaCl, 0.5% Na-Deoxycholate, 0.1% SDS, 2.5 mM EDTA pH = 8.0, 1 mM PMSF, and 1X Protease Inhibitor) at a concentration of 25E6 nuclei/mL.
Libraries were prepared using the KAPA Hyper Prep Kit (KAPA Biosystems, catalog KK8502) following the manufacturers protocol.


title: MPRA from SK-N-SH (ENCLB424NCN)

description:
https://www.encodeproject.org/experiments/ENCSR505LQA/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR505LQA
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB424NCN
fragmentation methods: none

value: cell line

value: not applicable

value: ENCBS494ICE at ENCODE; https://www.encodeproject.org/ENCBS494ICE/


title: pSPT5_Thr806P_DMSO_Serum5


title: PRO_dTAG_Serum0_Replicate1


title: MPRA from HEK293 (ENCLB142MIF)

description:
https://www.encodeproject.org/experiments/ENCSR481QRH/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR481QRH
assay title: MPRA
assembly: hg19
possible controls: ENCSR332LAV
encode release date: 2021-09-10
lab: Ryan Tewhey, JAX
library encode accession: ENCLB142MIF
fragmentation methods: none

value: female

value: ENCBS928OER at ENCODE; https://www.encodeproject.org/ENCBS928OER/


title: pSPT5_Thr806P_DMSO_Serum0


title: MPRA from HEK293 (ENCLB091LPT)

description:
https://www.encodeproject.org/experiments/ENCSR481QRH/
***************
biological replicate number: 5
technical replicate number: 1
description:
experiment encode accession: ENCSR481QRH
assay title: MPRA
assembly: hg19
possible controls: ENCSR332LAV
encode release date: 2021-09-10
lab: Ryan Tewhey, JAX
library encode accession: ENCLB091LPT
fragmentation methods: none

value: ENCBS324QAN at ENCODE; https://www.encodeproject.org/ENCBS324QAN/


title: SPT5_DMSO_Serum5


title: MPRA from HEK293 (ENCLB599BNQ)

description:
https://www.encodeproject.org/experiments/ENCSR481QRH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR481QRH
assay title: MPRA
assembly: hg19
possible controls: ENCSR332LAV
encode release date: 2021-09-10
lab: Ryan Tewhey, JAX
library encode accession: ENCLB599BNQ
fragmentation methods: none

value: ENCBS092NBF at ENCODE; https://www.encodeproject.org/ENCBS092NBF/


title: MPRA from HCT116 (ENCLB291VRC)

description:
https://www.encodeproject.org/experiments/ENCSR443ZPY/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR443ZPY
assay title: MPRA
assembly: hg19, GRCh38
possible controls: ENCSR836ULU
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB291VRC
fragmentation methods: none

source_name: Homo sapiens HCT116 cell line genetically modified (episome) using transient transfection, 24 hours post-nucleic acid delivery time

value: male

value: colorectal carcinoma

value: adult

value: 48 years

value: Ryan Tewhey, JAX

value: ENCBS977OTW at ENCODE; https://www.encodeproject.org/ENCBS977OTW/


title: CDK9_DMSO_Serum5


title: CDK9_dTAG_Serum5


title: MPRA from HEK293 (ENCLB198IKD)

description:
https://www.encodeproject.org/experiments/ENCSR481QRH/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR481QRH
assay title: MPRA
assembly: hg19
possible controls: ENCSR332LAV
encode release date: 2021-09-10
lab: Ryan Tewhey, JAX
library encode accession: ENCLB198IKD
fragmentation methods: none

value: ATCC

value: ENCBS749KEW at ENCODE; https://www.encodeproject.org/ENCBS749KEW/


title: MPRA from HCT116 (ENCLB098ZMF)

description:
https://www.encodeproject.org/experiments/ENCSR443ZPY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR443ZPY
assay title: MPRA
assembly: hg19, GRCh38
possible controls: ENCSR836ULU
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB098ZMF
fragmentation methods: none

value: ENCBS076QNW at ENCODE; https://www.encodeproject.org/ENCBS076QNW/


title: TFIIB_DMSO_Serum30


title: PRO_DMSO_Serum10_Replicate1


title: TFIIB_DMSO_Serum0


title: SPT5_dTAG_Serum5


title: MPRA from HCT116 (ENCLB386AMH)

description:
https://www.encodeproject.org/experiments/ENCSR443ZPY/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR443ZPY
assay title: MPRA
assembly: hg19, GRCh38
possible controls: ENCSR836ULU
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB386AMH
fragmentation methods: none

value: ENCBS412GBX at ENCODE; https://www.encodeproject.org/ENCBS412GBX/


title: MPRA from HCT116 (ENCLB248XXZ)

description:
https://www.encodeproject.org/experiments/ENCSR443ZPY/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR443ZPY
assay title: MPRA
assembly: hg19, GRCh38
possible controls: ENCSR836ULU
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB248XXZ
fragmentation methods: none

value: cell line

value: ENCBS371RFQ at ENCODE; https://www.encodeproject.org/ENCBS371RFQ/


title: TFIIB_dTAG_Serum30


title: SPT5_dTAG_Serum30


title: SPT5_DMSO_Serum30


title: MPRA from GM12878 (ENCLB489BIY)

description:
https://www.encodeproject.org/experiments/ENCSR410EJE/
***************
biological replicate number: 5
technical replicate number: 1
description:
experiment encode accession: ENCSR410EJE
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB489BIY
fragmentation methods: none

value: not applicable

value: unknown

value: Coriell

value: ENCBS795SCR at ENCODE; https://www.encodeproject.org/ENCBS795SCR/


title: MPRA from GM12878 (ENCLB139OZR)

description:
https://www.encodeproject.org/experiments/ENCSR410EJE/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR410EJE
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB139OZR
fragmentation methods: none

value: female

value: ENCBS789KAU at ENCODE; https://www.encodeproject.org/ENCBS789KAU/


title: SPT5_DMSO_Serum0


title: MPRA from HCT116 (ENCLB250PJD)

description:
https://www.encodeproject.org/experiments/ENCSR443ZPY/
***************
biological replicate number: 5
technical replicate number: 1
description:
experiment encode accession: ENCSR443ZPY
assay title: MPRA
assembly: hg19, GRCh38
possible controls: ENCSR836ULU
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB250PJD
fragmentation methods: none

value: male

value: colorectal carcinoma

value: ENCBS116BXA at ENCODE; https://www.encodeproject.org/ENCBS116BXA/


title: MED1_dTAG_Serum30


title: MED1_DMSO_Serum0


title: MED1_DMSO_Serum30


title: MPRA from GM12878 (ENCLB627OLW)

description:
https://www.encodeproject.org/experiments/ENCSR410EJE/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR410EJE
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB627OLW
fragmentation methods: none

value: adult

value: Ryan Tewhey, JAX

value: ENCBS717ZYV at ENCODE; https://www.encodeproject.org/ENCBS717ZYV/


title: MPRA from GM12878 (ENCLB599QKK)

description:
https://www.encodeproject.org/experiments/ENCSR410EJE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR410EJE
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB599QKK
fragmentation methods: none

value: ENCBS849FPW at ENCODE; https://www.encodeproject.org/ENCBS849FPW/


title: CDK7_dTAG_Serum30


title: CDK7_DMSO_Serum0


title: MPRA from SK-N-SH (ENCLB572ZTP)

description:
https://www.encodeproject.org/experiments/ENCSR386XIB/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR386XIB
assay title: MPRA
assembly: hg19, GRCh38
possible controls: ENCSR813IVZ
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB572ZTP
fragmentation methods: none

value: SK-N-SH

value: Metastatic neuroblastoma from bone marrow

value: child

value: 4 years

value: ATCC

value: ENCBS925FPN at ENCODE; https://www.encodeproject.org/ENCBS925FPN/


title: MPRA from SK-N-SH (ENCLB348WJJ)

description:
https://www.encodeproject.org/experiments/ENCSR386XIB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR386XIB
assay title: MPRA
assembly: hg19, GRCh38
possible controls: ENCSR813IVZ
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB348WJJ
fragmentation methods: none

value: cell line

value: not applicable

value: ENCBS028GJY at ENCODE; https://www.encodeproject.org/ENCBS028GJY/


title: MPRA from SK-N-SH (ENCLB207KNZ)

description:
https://www.encodeproject.org/experiments/ENCSR386XIB/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR386XIB
assay title: MPRA
assembly: hg19, GRCh38
possible controls: ENCSR813IVZ
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB207KNZ
fragmentation methods: none

value: female

value: ENCBS642SAO at ENCODE; https://www.encodeproject.org/ENCBS642SAO/


title: CDK9_dTAG_Serum30


title: MPRA from SK-N-SH (ENCLB911LTE)

description:
https://www.encodeproject.org/experiments/ENCSR386XIB/
***************
biological replicate number: 5
technical replicate number: 1
description:
experiment encode accession: ENCSR386XIB
assay title: MPRA
assembly: hg19, GRCh38
possible controls: ENCSR813IVZ
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB911LTE
fragmentation methods: none

value: ENCBS781ENK at ENCODE; https://www.encodeproject.org/ENCBS781ENK/


title: CDK7_DMSO_Serum30


title: MPRA from SK-N-SH (ENCLB636OEF)

description:
https://www.encodeproject.org/experiments/ENCSR386XIB/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR386XIB
assay title: MPRA
assembly: hg19, GRCh38
possible controls: ENCSR813IVZ
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB636OEF
fragmentation methods: none

value: ENCBS534SPF at ENCODE; https://www.encodeproject.org/ENCBS534SPF/


title: CDK9_DMSO_Serum30


title: MPRA from GM12878 (ENCLB083NHC)

description:
https://www.encodeproject.org/experiments/ENCSR368PIO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR368PIO
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB083NHC
fragmentation methods: none

value: unknown

value: adult

value: ENCBS536SLY at ENCODE; https://www.encodeproject.org/ENCBS536SLY/


title: MPRA from GM12878 (ENCLB393MUO)

description:
https://www.encodeproject.org/experiments/ENCSR368PIO/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR368PIO
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB393MUO
fragmentation methods: none

value: Ryan Tewhey, JAX

value: ENCBS447XVX at ENCODE; https://www.encodeproject.org/ENCBS447XVX/


title: PolII_Ser5P_dTAG_Serum30


title: CDK9_DMSO_Serum0


title: MPRA from K562 (ENCLB695ZBJ)

description:
https://www.encodeproject.org/experiments/ENCSR363XER/
***************
biological replicate number: 5
technical replicate number: 1
description:
experiment encode accession: ENCSR363XER
assay title: MPRA
assembly: hg19, GRCh38
possible controls: ENCSR830AFA
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB695ZBJ
fragmentation methods: none

value: chronic myelogenous leukemia (CML)

value: 53 years

value: ENCBS091KDS at ENCODE; https://www.encodeproject.org/ENCBS091KDS/


title: PolII_Ser5P_DMSO_Serum0


title: PolII_Ser2P_dTAG_Serum30_Replicate2


title: MPRA from GM12878 (ENCLB986FRI)

description:
https://www.encodeproject.org/experiments/ENCSR368PIO/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR368PIO
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB986FRI
fragmentation methods: none

value: ATCC

value: ENCBS888VOR at ENCODE; https://www.encodeproject.org/ENCBS888VOR/


title: MPRA from K562 (ENCLB483RFV)

description:
https://www.encodeproject.org/experiments/ENCSR363XER/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR363XER
assay title: MPRA
assembly: hg19, GRCh38
possible controls: ENCSR830AFA
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB483RFV
fragmentation methods: none

value: cell line

value: ENCBS864HNZ at ENCODE; https://www.encodeproject.org/ENCBS864HNZ/


title: MPRA from K562 (ENCLB223PGD)

description:
https://www.encodeproject.org/experiments/ENCSR363XER/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR363XER
assay title: MPRA
assembly: hg19, GRCh38
possible controls: ENCSR830AFA
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB223PGD
fragmentation methods: none

value: not applicable

value: ENCBS572AKM at ENCODE; https://www.encodeproject.org/ENCBS572AKM/


title: MPRA from GM12878 (ENCLB760SVR)

description:
https://www.encodeproject.org/experiments/ENCSR410EJE/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR410EJE
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB760SVR
fragmentation methods: none

value: female

value: Coriell

value: ENCBS088FYG at ENCODE; https://www.encodeproject.org/ENCBS088FYG/


title: MPRA from GM12878 (ENCLB100WRT)

description:
https://www.encodeproject.org/experiments/ENCSR368PIO/
***************
biological replicate number: 5
technical replicate number: 1
description:
experiment encode accession: ENCSR368PIO
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB100WRT
fragmentation methods: none

value: unknown

value: ENCBS675QWJ at ENCODE; https://www.encodeproject.org/ENCBS675QWJ/


title: MPRA from GM12878 (ENCLB410ZTP)

description:
https://www.encodeproject.org/experiments/ENCSR368PIO/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR368PIO
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB410ZTP
fragmentation methods: none

value: adult

value: ENCBS509ZOS at ENCODE; https://www.encodeproject.org/ENCBS509ZOS/


title: PolII_Ser5P_DMSO_Serum30


title: PolII_Ser2P_DMSO_Serum0_Replicate1


title: MPRA from K562 (ENCLB176ZMJ)

description:
https://www.encodeproject.org/experiments/ENCSR363XER/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR363XER
assay title: MPRA
assembly: hg19, GRCh38
possible controls: ENCSR830AFA
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB176ZMJ
fragmentation methods: none

value: Ryan Tewhey, JAX

value: ENCBS377HCR at ENCODE; https://www.encodeproject.org/ENCBS377HCR/


title: PolII_Ser2P_dTAG_Serum30_Replicate1


title: PolII_Ser2P_DMSO_Serum0_Replicate2